diff --git a/bin/pbsim b/bin/pbsim deleted file mode 100755 index 7a4a3da..0000000 Binary files a/bin/pbsim and /dev/null differ diff --git a/modules/pbsim/main.nf b/modules/pbsim/main.nf index 0ceea02..121ef0c 100644 --- a/modules/pbsim/main.nf +++ b/modules/pbsim/main.nf @@ -6,6 +6,8 @@ process PBSIM { // Store results publishDir "${params.outdir}", mode: 'copy', pattern: "simulated_hap${sample}.ONTWGS*.fastq" + conda "bioconda::pbsim3=3.0.4" + // Process I/O input: tuple val(sample), path(fasta) @@ -17,7 +19,7 @@ process PBSIM { script: unique_seed = (params.seed * sample) % 2147483647 // that's (2^31)-1, the upper bound for mason """ - ${projectDir}/${params.pbsim_bin} \ + pbsim \ --seed ${unique_seed} \ --strategy ${params.pbsim_strategy} \ --prefix simulated_hap${sample}.ONTWGS \ diff --git a/nextflow.config b/nextflow.config index f972615..e3169ec 100644 --- a/nextflow.config +++ b/nextflow.config @@ -35,7 +35,6 @@ params { nb_reads = 10000 // PBSIM Oxford Nanopore (WGS) - Read simulation parameters - pbsim_bin = 'bin/pbsim' pbsim_method = 'qshmm' pbsim_model = 'aux/pbsim_model/QSHMM-ONT-HQ.model' pbsim_depth = 500